I am not certain about this, but I think that the problem with the urease structure is the atom and bond types (c -n1-c3) in the bonds connecting the CME residue with an adjacent residue.  CME is the unusual residue S,S-(2-hydroxyethyl)thiocysteine. One way to deal with the issue is to manually enter the atom and bond types and update the force field files. You could also contact CCG MOE technical support for instructions.

Please I need full procedures I am new user for MOE

and I want to dock my newly synthesized compounds into the urease enzyme

or if you have the MOE program could you send me the prepared enzyme ready for docking 

I will be appreciated 

than you

Previously, I used MOE, but I did not renew my license. I now use YASARA-Structure as a front-end to Autodock and Autodock Vina for docking.

Which urease structure are you using?

I had a trial version of MOE and there are some parameters should be fixed to have perfect docking procedures, So could I have your e-mail to send you some screen shots to guide me wuth procedures? 

I will be appreciated

I am using 1E9Y H.Pylori urease 

If you do not have a full license to MOE, I suggest switching to a freely available docking program, such as Autodock or Autodock Vina. In addition, unlike some of the structures for urease in the PDB, the 1E9Y structure does not contain atom and/or bond types that are not found in the AMBER force fields, so that it is not necessary to add parameters to the force field files. Therefore, docking should be straightforward using Autodock or Autodock Vina.

Yes I prefer MOE I have a trial version with all properties until the end or April 

So I prefer to use MOE 

I tried Autodock but it is not easy to perform docking

I seldom see MOE used for docking. However,  I do agree with a paper from CCG MOE indicating that the quality of docking results is highly dependent, among other things, on the care spent in the preparation of ligands and receptors for docking.

i will try